57 rubella virus strains were isolated using Vero cell line or Vero/SLAM cell line from patients' throat swabs during rubella outbreaks and sporadics in 10 provinces of China from 2003 to 2007. Fragments of 1107 nucleotides of E1 genes of the isolates were amplified by RT-PCR, the PCR products were directly sequenced and analyzed. The phylogenetic analysis based on 739 nucleotides showed that out of 57 Chinese rubella virus strains, 55 belong to a distinguish branch of 1E genotype when comparing with 1E genotype rubella strains from other countries, and the other 2 Chinese rubella virus strains belong to 2B genotype. Most of the nucleotide mutations of 57 rubella viruses were silent mutations, and the amino acid sequences were highly conserved. Except one amino acid change (Thr212 --> Ser212) in two rubella viruses at the hemagglutination inhibition and neutralization epitopes, there had no change found at the important antigenic epitope sites of the other rubella viruses. 1E genotype rubella viruses isolated from 10 provinces of China from 2003 to 2007, and two imported 2B genotype rubella viruses from Vietnam suggested that 1E genotype was the predominant genotype in this period of time. The rubella virus genotypes circulated during 2003 to 2007 were different from that circulating during 1979 to 1984 and 1999 to 2002, the rubella prevailed in recent years was mainly caused by 1E genotype rubella viruses with multi-transmission routes.